/******************************************************************************
* This function creates an instance of a data block reader UDT for reading
* priors from a MEME PSP file.
*****************************************************************************/
DATA_BLOCK_READER_T *new_prior_reader_from_psp(const char *filename) {
PSP_DATA_BLOCK_READER_T *psp_reader = mm_malloc(sizeof(PSP_DATA_BLOCK_READER_T) * 1);
psp_reader->at_start_of_line = TRUE;
int filename_len = strlen(filename) + 1;
psp_reader->filename = mm_malloc(sizeof(char)* filename_len);
psp_reader->filename_len = filename_len;
strncpy(psp_reader->filename, filename, filename_len);
psp_reader->sequence_header = NULL;
psp_reader->sequence_header_len = 0;
psp_reader->psp_file = fopen(psp_reader->filename, "r");
if (psp_reader->psp_file == NULL) {
die(
"Unable to open file: %s.\nError message: %s.\n",
psp_reader->filename,
strerror(errno)
);
}
DATA_BLOCK_READER_T *reader = new_data_block_reader(
(void *) psp_reader,
free_prior_reader_from_psp,
close_prior_reader_from_psp,
reset_prior_reader_from_psp,
get_next_data_block_from_prior_reader_from_psp,
go_to_next_sequence_in_prior_reader_from_psp,
get_seq_name_from_prior_reader_from_psp
);
return reader;
}
/******************************************************************************
* This function creates an instance of a data block reader UDT for reading
* priors from a wiggle file.
*****************************************************************************/
DATA_BLOCK_READER_T *new_prior_reader_from_wig(
const char *filename,
double default_prior
) {
WIGGLE_READER_T *raw_reader = new_wiggle_reader(filename);
WIG_PRIOR_BLOCK_READER_T *wig_reader = mm_malloc(sizeof(WIG_PRIOR_BLOCK_READER_T) * 1);
wig_reader->raw_reader = raw_reader;
wig_reader->current_position = 0;
wig_reader->default_prior = default_prior;
wig_reader->sequence_name = NULL;
// Setup "Virtual" function table
DATA_BLOCK_READER_T *reader = new_data_block_reader(
(void *) wig_reader,
free_prior_reader_from_wig,
close_prior_reader_from_wig,
reset_prior_reader_from_wig,
prior_reader_from_wig_is_eof,
get_next_data_block_from_wig,
unget_data_block_from_wig,
go_to_next_sequence_in_wiggle_reader,
get_seq_name_from_wig
);
return reader;
}
/******************************************************************************
* This function creates an instance of a data block reader UDT for reading
* sequence segments from a FASTA file.
*****************************************************************************/
DATA_BLOCK_READER_T *new_seq_reader_from_fasta(
BOOLEAN_T parse_genomic_coord,
ALPH_T alph,
const char *filename
) {
SEQ_READER_FROM_FASTA_T *fasta_reader = mm_malloc(sizeof(SEQ_READER_FROM_FASTA_T) * 1);
fasta_reader->at_start_of_line = TRUE;
fasta_reader->parse_genomic_coord = parse_genomic_coord;
int filename_len = strlen(filename) + 1;
fasta_reader->filename = mm_malloc(sizeof(char)* filename_len);
fasta_reader->filename_len = filename_len;
strncpy(fasta_reader->filename, filename, filename_len);
fasta_reader->current_position = 0;
fasta_reader->sequence_header = NULL;
fasta_reader->sequence_header_len = 0;
fasta_reader->sequence_name = NULL;
fasta_reader->sequence_name_len = 0;
fasta_reader->alphabet = alph;
if (
open_file(
filename,
"r",
TRUE,
"FASTA",
"sequences",
&(fasta_reader->fasta_file
)) == FALSE) {
die("Couldn't open the file %s.\n", filename);
}
DATA_BLOCK_READER_T *reader = new_data_block_reader(
(void *) fasta_reader,
free_seq_reader_from_fasta,
close_seq_reader_from_fasta,
reset_seq_reader_from_fasta,
seq_reader_from_fasta_is_eof,
get_next_data_block_from_seq_reader_from_fasta,
go_to_next_sequence_in_seq_reader_from_fasta,
get_seq_name_from_seq_reader_from_fasta
);
return reader;
}
